Tricholoma matsutake (S. Ito et Imai) is an ectomycorrhizal basidiomycete associated with Pinaceae and Fagaceae trees in the Northern Hemisphere. It is still unknown whether the symbiotic relationship with this ectomycorrhiza could affect the host plant's endophytic microbial community. In this study, we used high throughput sequencing to analyze the endophytic microbial communities of different Quercus aquifolioides tissues with or without T. matsutake partner. About 35,000 clean reads were obtained per sample, representing 34 bacterial phyla and 7 fungal phyla. We observed 3980 operational taxonomic units (OTUs) of bacteria and 457 OTUs of fungi at a 97% similarity level. Three bacterial phyla, Proteobacteria, Cyanobacteria, and Bacteroidetes, and the fungal phylum Ascomycota were dominant in all tissues. The relative abundance of these taxa differed significantly between Q. aquifolioides tissues with and without T. matsutake partner (p < 0.05). The bacterial genus Pseudomonas and the fungal genus Cryptosporiopsis were more abundant in mycorrhized roots than in control roots. This study showed that the community structure and dominant species of endophytic microbial communities in Q. aquifolioides tissues might be altered by colonization with T. matsutake. This work provides a new insight into the interactions between ectomycorrhizal fungus and host plant.